You learn atemi period. and you should learn good atemi. Good atemi done correctly will get the job done...and it may killl or not kill...that depends on many factors...but in the end...the atemi is the same.
The tendency to attach philosophical and moral questions to these things is a good discussion for those so inclined. And I do believe that Aikido, at least on some level of understanding, involves a struggle with those issues. However, there are some serious issues here if the person in question is incapable of delivering the technique except with "complicit" partners in a dojo. In that case the atemi is worthless and is really just part of a cooperative "dance" that will make no sense in contexts other than a dojo. The mugger on the street will not be phased by a tap. Depending on what they've ingested they might not even be phased by a pretty good shot to the chest. Things get complicated and messy in the "real world" (patent pending).
There are many within aikido who practice in a fashion that brings to mind a famous quote by Gandhi.
It is better to be violent, if there is violence in our hearts, than to put on the cloak of nonviolence to cover impotence. -- Mahatma Gandhi
Some would do well to understand what he is saying. Lots of people wear that cloak like a medal, proudly proclaiming their transcendent ability. Unfortunately the fella attacking may not be in the same transcendent state when they try to take your head off.
Anyway, I think it is a somewhat an error to think about the atemi as a "killing blow". It is an atemi. *In context* it could be many things depending *on* that context. Sure, once we have developed tremendous skill we might have the choice of how we go about delivering our atemi in that sense in the larger context. Unfortunately many skip all that messy "getting good at it" stuff and hope that the philosophy without the foundation will be good enough. And I dare say it is only good enough when the guy attacking is already keyed in on your rules.
So philosophical or practical martial art? Um, how about start with the martial art. Study the philosophy. Get good at the former, and learn the latter. They should come together in the end. But to insist one, the other, both, whatever seems to me to be oversimplifying a really complex issue. And it is often done at the expense of one or the other.
So no answers from me. Really I suppose I'm saying the question really doesn't make a whole lot of sense because it tends to imply a necessity of choosing. As if there aren't overlaps, differences, and context sensitive issues to contend with. It ain't so simple... To me at least.